是否可以在snakemake的rule all中加入条件语句？

Question

我想运行多个名为 qc.smk 、dada2.smk、picrust2.smk 的蛇文件使用奇点。然后有一个名为 longitudinal.smk 的 snakefile，我想有条件地运行。例如，如果纵向数据是正在使用。

# set vars

LONGITUDINAL = config['perform_longitudinal']

rule all:
  input:
    # fastqc output before trimming
    raw_html = expand("{scratch}/fastqc/{sample}_{num}_fastqc.html", scratch = SCRATCH, sample=SAMPLE_SET, num=SET_NUMS),
    raw_zip = expand("{scratch}/fastqc/{sample}_{num}_fastqc.zip", scratch = SCRATCH, sample=SAMPLE_SET, num=SET_NUMS),
    raw_multi_html = SCRATCH + "/fastqc/raw_multiqc.html",
    raw_multi_stats = SCRATCH + "/fastqc/raw_multiqc_general_stats.txt"

# there are many more files in rule all

##### setup singularity #####

singularity: "docker://continuumio/miniconda3"

##### load rules #####

include: "rules/qc.smk"
include: "rules/dada2.smk"
include: "rules/phylogeny.smk"
include: "rules/picrust2.smk"

if LONGITUDINAL == 'yes':
    include: 'rules/longitudinal.smk'
    print("Will perform a longitudinal analysis")
else:
    print("no longitudinal analysis")

以上代码仅在我运行纵向数据集时有效。但是，当我不运行ning 时，纵向分析 snakemake 失败并显示类似：

MissingInputException in line 70 of /mnt/c/Users/noahs/projects/tagseq-qiime2-snakemake-1/Snakefile:
Missing input files for rule all:

我想如果我能够添加一个类似的条件语句，就像我为我的外部 snakefile 设置的那样，snakemake 就不会因为我不包括纵向 snakefile 而感到害怕。

Answer 1

您可以在 rule all 之外定义一个您想要的输出列表（或字典），并将其提供给输入，这样的方法可行：

myoutput = list()

if condition_1 == True:
    myoutput.append("file_1.txt")
if condition_2 == True:
    myoutput.append("file_2.txt")

rule all:
    input:
        myoutput

编辑：

将myoutput放在规则全部输入的第一位：

rule all:
    input:
        myoutput,
        raw_html = "raw_html_path",
        raw_zip = "raw_zip_path"

或者给它命名，然后把它放在任何地方：

rule all:
    input:
        raw_html = "raw_html_path",
        myoutput = myoutput,
        raw_zip = "raw_zip_path"

在 Python（和 snakemake）中，命名位置参数总是在命名参数之前。

Answer 2

合并列表形式扩展语句的解决方法：

我使用配置文件将语句传递给 Snakefile

## Config.yml ##
# longitudinal analysis
perform_longitudinal: 'yes' # yes for longitudinal analysis

当在配置中输入 'yes' 时，Snakemake 将在规则 all 中包含其他变量，并运行添加一个 Snakefile 来生成这些文件。最终有多个 Snakefile，所以我使用奇点让 Snakemake 知道规则所有输入文件都适用于所有 6 个 Snakefile。

## Snakefile ##

configfile: "config.yaml"

LONGITUDINAL = config['perform_longitudinal']

 # rule all input files
 raw_html=file.txt, 
 raw_zip=file.txt,
 raw_multi_htmt=file.txt,
 raw_multi_stats=file.txt,
 Longitudinal_analaysis_files=file.txt

# rule all files excluding longitudinal analysis
rule_all_input_list=['raw_html','raw_zip','raw_multi_htmt','raw_multi_stats']

#longitudinal analysis files
rule_all_longitudinal_input=['Longitudinal_analaysis_files']

if LONGITUDINAL == 'yes':

    rule_all_input_list.extend(rule_all_longitudinal_input)

# conditionally add Snakefile to workflow
    include: 'rules/longitudinal.smk'

    print("Will perform a longitudinal analysis")

else:
    print("no longitudinal analysis")


rule all:
    input:
        data = rule_all_input_list

##### setup singularity #####

# this container defines the underlying OS for each job when using the workflow
# with --use-conda --use-singularity
singularity: "docker://continuumio/miniconda3"

##### load rules #####

include: "rules/qc.smk"
include: "rules/dada2.smk"
include: "rules/phylogeny.smk"
include: "rules/picrust2.smk"
include: "rules/differential.smk"

我有一个不太简单的版本来说明我是如何工作的 GitHub https://github.com/nasiegel88/tagseq-qiime2-snakemake-1

是否可以在snakemake的rule all中加入条件语句？

Is it possible to add a conditional statement in snakemake's rule all?

python

qiime

snakemake